Variant report

Variant	rs1590628
Chromosome Location	chr9:22263376-22263377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10757302	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10757303	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10757304	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10757305	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10757306	0.83[AMR][1000 genomes]
rs10811688	0.83[AMR][1000 genomes]
rs10811689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs10965327	0.92[YRI][hapmap]
rs1327045	1.00[CHB][hapmap]
rs1327046	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1327049	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1327054	0.80[AMR][1000 genomes]
rs1359740	0.86[AMR][1000 genomes]
rs1575964	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1590629	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1590630	1.00[CEU][hapmap]
rs1620570	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1625388	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1625409	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1679018	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1679020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1679022	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1679024	0.91[EUR][1000 genomes]
rs1679026	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1679028	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16905917	1.00[JPT][hapmap]
rs1751435	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1751437	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1751438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1751450	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1751452	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1751453	0.91[EUR][1000 genomes]
rs2025798	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2383216	0.83[AMR][1000 genomes]
rs4246844	1.00[CEU][hapmap]
rs4246845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs4256664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs4292787	0.86[AMR][1000 genomes]
rs6475627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7037085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7847069	0.80[AMR][1000 genomes]
rs7871143	0.86[AMR][1000 genomes]
rs9298834	0.80[AMR][1000 genomes]
rs9298835	0.80[AMR][1000 genomes]
rs943394	0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1021264	chr9:22159622-22293804	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1033789	chr9:22183150-22266091	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015364	chr9:22211364-22416886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv540086	chr9:22211364-22416886	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1023972	chr9:22246764-22426267	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv540087	chr9:22246764-22426267	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22259200-22263800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:22261200-22265200	Weak transcription	A549	lung

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